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Abstract

It is becoming increasingly clear that a large repertoire of noncoding RNAs (ncRNAs) are actively transcribed from the mammalian genome, regulating diverse cellular processes in development and diseases through a variety of gene regulatory mechanisms. As the most extensively studied ncRNA species, microRNAs (miRNAs) are important components in the oncogene and tumor suppressor network, and have been employed as potential biomarkers, therapeutic reagents, and therapeutic targets for cancer treatment. Other ncRNAs, particularly long noncoding RNAs, also have a profound impact on cancer development, as demonstrated in both mouse and human tumor models. We are only starting to understand the realm of ncRNA biology, and the exact molecular mechanisms governing ncRNA functions remain largely unexplored. With numerous ncRNAs discovered through high-throughput approaches, understanding their functions in malignant transformation will be one of the most exciting challenges in cancer research.

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2017-03-06
2024-04-22
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Literature Cited

  1. Agarwal V, Bell GW, Nam J-W, Bartel DP. 2015. Predicting effective microRNA target sites in mammalian mRNAs. eLife 4:e05005 [Google Scholar]
  2. Agrelo R, Souabni A, Novatchkova M, Haslinger C, Leeb M. et al. 2009. SATB1 defines the developmental context for gene silencing by Xist in lymphoma and embryonic cells. Dev. Cell 16:507–16 [Google Scholar]
  3. Arun G, Diermeier S, Akerman M, Chang K-C, Wilkinson JE. et al. 2016. Differentiation of mammary tumors and reduction in metastasis upon Malat1 lncRNA loss. Genes Dev 30:34–51 [Google Scholar]
  4. Assumpção CB, Calcagno DQ, Araújo TM, Santos SE, Santos AK. et al. 2015. The role of piRNA and its potential clinical implications in cancer. Epigenomics 7:975–84 [Google Scholar]
  5. Babar IA, Cheng CJ, Booth CJ, Liang X, Weidhaas JB. et al. 2012. Nanoparticle-based therapy in an in vivo microRNA-155 (miR-155)-dependent mouse model of lymphoma. PNAS 109:E1695–704 [Google Scholar]
  6. Bagga S, Bracht J, Hunter S, Massirer K, Holtz J. et al. 2005. Regulation by let-7 and. lin-4 miRNAs results in target mRNA degradation. Cell 122:553–63 [Google Scholar]
  7. Balbin OA, Malik R, Dhanasekaran SM, Prensner JR, Cao X. et al. 2015. The landscape of antisense gene expression in human cancers. Genome Res 25:1068–79 [Google Scholar]
  8. Bernstein E, Caudy AA, Hammond SM, Hannon GJ. 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409:363–66 [Google Scholar]
  9. Bosson AD, Zamudio JR, Sharp PA. 2014. Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition. Mol. Cell 56:347–59 [Google Scholar]
  10. Brennecke J, Stark A, Russell RB, Cohen SM. 2005. Principles of microRNA-target recognition. PLOS Biol 3:e85 [Google Scholar]
  11. Brown CJ, Ballabio A, Rupert JL, Lafreniere RG, Grompe M. et al. 1991. A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature 349:38–44 [Google Scholar]
  12. Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S. et al. 2002. Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. PNAS 99:15524–29 [Google Scholar]
  13. Calin GA, Sevignani C, Dumitru CD, Yslop T, Noch E. et al. 2004. Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. PNAS 101:2999–3004 [Google Scholar]
  14. Calin GA, Liu CG, Ferracin M, Hyslop T, Spizzo R. et al. 2007. Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell 12:215–29 [Google Scholar]
  15. Calin GA, Croce CM. 2006. MicroRNA signatures in human cancers. Nat. Rev. Cancer 6:857–66 [Google Scholar]
  16. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC. et al. 2005. The transcriptional landscape of the mammalian genome. Science 309:1559–63 [Google Scholar]
  17. Chang T-C, Wentzel EA, Kent OA, Ramachandran K, Mullendore M. et al. 2007. Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis. Mol. Cell 26:745–52 [Google Scholar]
  18. Cheng CJ, Bahal R, Babar IA, Pincus Z, Barrera F. et al. 2015. MicroRNA silencing for cancer therapy targeted to the tumour microenvironment. Nature 518:107–10 [Google Scholar]
  19. Chi SW, Zang JB, Mele A, Darnell RB. 2009. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460:479–86 [Google Scholar]
  20. Chiefari E, Iiritano S, Paonessa F, Le Pera I, Arcidiacono B. et al. 2010. Pseudogene-mediated posttranscriptional silencing of HMGA1 can result in insulin resistance and type 2 diabetes. Nat. Commun. 1:40 [Google Scholar]
  21. Choi YJ, Lin C-P, Ho JJ, He X, Okada N. et al. 2011. miR-34 miRNAs provide a barrier for somatic cell reprogramming. Nat. Cell Biol. 13:1353–60 [Google Scholar]
  22. Clurman BE, Hayward WS. 1989. Multiple proto-oncogene activations in avian leukosis virus-induced lymphomas: evidence for stage-specific events. Mol. Cell. Biol. 9:2657–64 [Google Scholar]
  23. Concepcion CP, Han Y-C, Mu P, Bonetti C, Yao E. et al. 2012. Intact p53-dependent responses in miR-34-deficient mice. PLOS Genet 8:e1002797 [Google Scholar]
  24. Conkrite K, Sundby M, Mukai S, Thomson JM, Mu D. et al. 2011. miR-17∼92 cooperates with RB pathway mutations to promote retinoblastoma. Genes Dev. 25:1734–45 [Google Scholar]
  25. Costinean S, Zanesi N, Pekarsky Y, Tili E, Volinia S. 2006. Pre-B cell proliferation and lymphoblastic leukemia/high-grade lymphoma in Eμ-miR 155 transgenic mice. PNAS 103:7024–29 [Google Scholar]
  26. Costinean S, Sandhu SK, Pedersen IM, Tili E, Trotta R. et al. 2009. Src homology 2 domain-containing inositol-5-phosphatase and CCAAT enhancer-binding protein β are targeted by miR-155 in B cells of Eμ-MiR-155 transgenic mice. Blood 114:1374–82 [Google Scholar]
  27. Cui B, Chen L, Zhang S, Mraz M, Fecteau J-F. et al. 2014. MicroRNA-155 influences B-cell receptor signaling and associates with aggressive disease in chronic lymphocytic leukemia. Blood 124:546–54 [Google Scholar]
  28. Cunnington MS, Santibanez Koref M, Mayosi BM, Burn J, Keavney B. 2010. Chromosome 9p21 SNPs associated with multiple disease phenotypes correlate with ANRIL expression. PLOS Genet 6:e1000899 [Google Scholar]
  29. Denzler REM, Agarwal V, Stefano J, Bartel DP, Stoffel M. 2014. Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance. Mol. Cell 54:766–76 [Google Scholar]
  30. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S. et al. 2012. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22:1775–89 [Google Scholar]
  31. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T. et al. 2012. Landscape of transcription in human cells. Nature 489:101–8 [Google Scholar]
  32. Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA. et al. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74 [Google Scholar]
  33. Dykxhoorn DM, Wu Y, Xie H, Yu F, Lal A. et al. 2009. miR-200 enhances mouse breast cancer cell colonization to form distant metastases. PLOS ONE 4:e7181 [Google Scholar]
  34. Eis PS, Tam W, Sun L, Chadburn A, Li Z. et al. 2005. Accumulation of miR-155 and BIC RNA in human B cell lymphomas. PNAS 102:3627–32 [Google Scholar]
  35. Eißmann M, Gutschner T, Hämmerle M, Günther S, Caudron-Herger M. et al. 2012. Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development. RNA Biol 9:1076–87 [Google Scholar]
  36. El Messaoudi-Aubert S, Nicholls J, Maertens GN, Brookes S, Bernstein E, Peters G. 2010. Role for the MOV10 RNA helicase in polycomb-mediated repression of the INK4a tumor suppressor. Nat. Struct. Mol. Biol. 17:862–68 [Google Scholar]
  37. Esquela-Kerscher A, Trang P, Wiggins JF, Patrawala L, Cheng A. et al. 2008. The let-7 microRNA reduces tumor growth in mouse models of lung cancer. Cell Cycle 7:759–64 [Google Scholar]
  38. Esteller M. 2011. Non-coding RNAs in human disease. Nat. Rev. Genet. 12:861–74 [Google Scholar]
  39. Fang Y, Fullwood MJ. 2016. Roles, functions, and mechanisms of long non-coding RNAs in cancer. Genom. Proteom. Bioinform. 14:42–54 [Google Scholar]
  40. Ferrajoli A, Shanafelt TD, Ivan C, Shimizu M, Rabe KG. et al. 2013. Prognostic value of miR-155 in individuals with monoclonal B-cell lymphocytosis and patients with B-chronic lymphocytic leukemia. Blood 122:1891–99 [Google Scholar]
  41. Fischer KR, Durrans A, Lee S, Sheng J, Li F. et al. 2015. Epithelial-to-mesenchymal transition is not required for lung metastasis but contributes to chemoresistance. Nature 527:472–76 [Google Scholar]
  42. Förstemann K, Horwich MD, Wee L, Tomari Y, Zamore PD. 2007. Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by dicer-1. Cell 130:287–97 [Google Scholar]
  43. Furlan G, Rougeulle C. 2016. Function and evolution of the long noncoding RNA circuitry orchestrating X-chromosome inactivation in mammals. Wiley Interdiscip. Rev. RNA 7:702–22 [Google Scholar]
  44. Gibbons DL, Lin W, Creighton CJ, Rizvi ZH, Gregory PA. et al. 2009. Contextual extracellular cues promote tumor cell EMT and metastasis by regulating miR-200 family expression. Genes Dev 23:2140–51 [Google Scholar]
  45. Gil JUS, Peters G. 2006. Regulation of the INK4b-ARF-INK4a tumour suppressor locus: all for one or one for all. Nat. Rev. Mol. Cell Biol. 7:667–77 [Google Scholar]
  46. Goodarzi H, Liu X, Nguyen HCB, Zhang S, Fish L, Tavazoie SF. 2015. Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement. Cell 161:790–802 [Google Scholar]
  47. Green D, Fraser WD, Dalmay T. 2016. Transfer RNA-derived small RNAs in the cancer transcriptome. Pflugers Arch 468:1041–47 [Google Scholar]
  48. Gregory PA, Bert AG, Paterson EL, Barry SC, Tsykin A. et al. 2008. The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1. Nat. Cell Biol. 10:593–601 [Google Scholar]
  49. Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B. et al. 2004. The microprocessor complex mediates the genesis of microRNAs. Nature 432:235–40 [Google Scholar]
  50. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP. et al. 2007. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell. 27:91–105 [Google Scholar]
  51. Guo H, Ingolia NT, Weissman JS, Bartel DP. 2010. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466:835–40 [Google Scholar]
  52. Gutschner T, Diederichs S. 2012. The hallmarks of cancer: a long non-coding RNA point of view. RNA Biol 9:703–19 [Google Scholar]
  53. Gutschner T, Hämmerle M, Eißmann M, Hsu J, Kim Y. et al. 2013. The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells. Cancer Res 73:1180–89 [Google Scholar]
  54. Hagan JP, Piskounova E, Gregory RI. 2009. Lin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in mouse embryonic stem cells. Nat. Struct. Mol. Biol. 16:1021–25 [Google Scholar]
  55. Han J, Lee Y, Yeom K-H, Kim Y-K, Jin H, Kim VN. 2004. The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev 18:3016–27 [Google Scholar]
  56. Han Y-C, Vidigal JA, Mu P, Yao E, Singh I. et al. 2015. An allelic series of miR-17∼92-mutant mice uncovers functional specialization and cooperation among members of a microRNA polycistron. Nat. Genet. 47:766–75 [Google Scholar]
  57. Hanahan D, Weinberg RA. 2011. Hallmarks of cancer: the next generation. Cell 144:646–74 [Google Scholar]
  58. Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B. et al. 2013. Natural RNA circles function as efficient microRNA sponges. Nature 495:384–88 [Google Scholar]
  59. Hayashita Y, Osada H, Tatematsu Y, Yamada H, Yanagisawa K. et al. 2005. A polycistronic microRNA cluster, miR-17-92, is overexpressed in human lung cancers and enhances cell proliferation. Cancer Res 65:9628–32 [Google Scholar]
  60. Hayes J, Peruzzi PP, Lawler S. 2014. MicroRNAs in cancer: biomarkers, functions and therapy. Trends Mol. Med. 20:460–69 [Google Scholar]
  61. He L, He X, Lim LP, de Stanchina E, Xuan Z. et al. 2007. A microRNA component of the p53 tumour suppressor network. Nature 447:1130–34 [Google Scholar]
  62. He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D. et al. 2005. A microRNA polycistron as a potential human oncogene. Nature 435:828–33 [Google Scholar]
  63. Heo I, Joo C, Cho J, Ha M, Han J. et al. 2008. Lin28 mediates the terminal uridylation of let-7 precursor microRNA. Mol. Cell 32:276–84 [Google Scholar]
  64. Heo I, Joo C, Kim Y-K, Ha M, Yoon M-J. et al. 2009. TUT4 in concert with Lin28 suppresses microRNA biogenesis through pre-microRNA uridylation. Cell 138:696–708 [Google Scholar]
  65. Hermeking H. 2010. The miR-34 family in cancer and apoptosis. Cell Death Differ 17:193–99 [Google Scholar]
  66. Hong L, Lai M, Chen M, Xie C, Liao R. et al. 2010. The miR-17-92 cluster of microRNAs confers tumorigenicity by inhibiting oncogene-induced senescence. Cancer Res 70:8547–57 [Google Scholar]
  67. Huang Y-S, Chang C-C, Lee S-S, Jou Y-S, Shih H-M. 2016. Xist reduction in breast cancer upregulates AKT phosphorylation via HDAC3-mediated repression of PHLPP1 expression. Oncotarget. 743256–66
  68. Hutvágner G, McLachlan J, Pasquinelli AE, Bálint E, Tuschl T. et al. 2001. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293:834–38 [Google Scholar]
  69. Iorio MV, Croce CM. 2012. MicroRNA dysregulation in cancer: diagnostics, monitoring and therapeutics. A comprehensive review. EMBO Mol. Med. 4:143–59 [Google Scholar]
  70. Ji P, Diederichs S, Wang W, Böing S, Metzger R. et al. 2003. MALAT-1, a novel noncoding RNA, and thymosin β4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene 22:8031–41 [Google Scholar]
  71. Ji Y, Wrzesinski C, Yu Z, Hu J, Gautam S. et al. 2015. miR-155 augments CD8+ T-cell antitumor activity in lymphoreplete hosts by enhancing responsiveness to homeostatic βγc cytokines. PNAS 112:476–81 [Google Scholar]
  72. Johnson SM, Grosshans H, Shingara J, Byrom M, Jarvis R. et al. 2005. RAS is regulated by the let-7 microRNA family. Cell 120:635–47 [Google Scholar]
  73. Johnsson P, Ackley A, Vidarsdottir L, Lui WO, Corcoran M. et al. 2013. A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells. Nat. Struct. Mol. Biol. 20:440–46 [Google Scholar]
  74. Kalyana-Sundaram S, Kumar-Sinha C, Shankar S, Robinson DR, Wu Y-M. et al. 2012. Expressed pseudogenes in the transcriptional landscape of human cancers. Cell 149:1622–34 [Google Scholar]
  75. Karreth FA, Reschke M, Ruocco A, Ng C, Chapuy B. et al. 2015. The BRAF pseudogene functions as a competitive endogenous RNA and induces lymphoma in vivo. Cell 161:319–32 [Google Scholar]
  76. Kasinski AL, Slack FJ. 2012. miRNA-34 prevents cancer initiation and progression in a therapeutically resistant K-ras and p53-induced mouse model of lung adenocarcinoma. Cancer Res 72:5576–87 [Google Scholar]
  77. Kim VN, Han J, Siomi MC. 2009. Biogenesis of small RNAs in animals. Nat. Rev. Mol. Cell Biol. 10:126–39 [Google Scholar]
  78. Kirchner S, Ignatova Z. 2014. Emerging roles of tRNA in adaptive translation, signalling dynamics and disease. Nat. Rev. Genet. 16:98–112 [Google Scholar]
  79. Knezevic J, Pfefferle AD, Petrovic I, Greene SB, Perou CM, Rosen JM. 2015. Expression of miR-200c in claudin-low breast cancer alters stem cell functionality, enhances chemosensitivity and reduces metastatic potential. Oncogene 34:5997–6006 [Google Scholar]
  80. Korpal M, Ell BJ, Buffa FM, Ibrahim T, Blanco MA. et al. 2011. Direct targeting of Sec 23a by miR-200s influences cancer cell secretome and promotes metastatic colonization. Nat. Med. 17:1101–8 [Google Scholar]
  81. Korpal M, Lee ES, Hu G, Kang Y. 2008. The miR-200 family inhibits epithelial-mesenchymal transition and cancer cell migration by direct targeting of E-cadherin transcriptional repressors ZEB1. ZEB2. J. Biol. Chem. 283:14910–14 [Google Scholar]
  82. Kotake Y, Nakagawa T, Kitagawa K, Suzuki S, Liu N. et al. 2011. Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15INK4B tumor suppressor gene. Oncogene 30:1956–62 [Google Scholar]
  83. Kumar MS, Pester RE, Chen CY, Lane K, Chin C. et al. 2009. Dicer1 functions as a haploinsufficient tumor suppressor. Genes Dev 23:2700–4 [Google Scholar]
  84. Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T. 2002. Identification of tissue-specific microRNAs from mouse. Curr. Biol. 12:735–39 [Google Scholar]
  85. Lambertz I, Nittner D, Mestdagh P, Denecker G, Vandesompele J. et al. 2010. Monoallelic but not biallelic loss of Dicer1 promotes tumorigenesis in vivo. Cell Death Differ 17:633–41 [Google Scholar]
  86. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC. et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860–921 [Google Scholar]
  87. Landthaler M, Yalcin A, Tuschl T. 2004. The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis. Curr. Biol. 14:2162–67 [Google Scholar]
  88. Latos PA, Pauler FM, Koerner MV, Şenergin HB, Hudson QJ. et al. 2012. Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing. Science 338:1469–72 [Google Scholar]
  89. Le MTN, Hamar P, Guo C, Basar E, Perdigão-Henriques R. et al. 2014. miR-200-containing extracellular vesicles promote breast cancer cell metastasis. J. Clin. Invest. 124:5109–28 [Google Scholar]
  90. Lee S, Kopp F, Chang T-C, Sataluri A, Chen B. et al. 2016. Noncoding RNA NORAD regulates genomic stability by sequestering PUMILIO proteins. Cell 164:69–80 [Google Scholar]
  91. Lee Y, Ahn C, Han J, Choi H, Kim J. et al. 2003. The nuclear RNase III Drosha initiates microRNA processing. Nature 425:415–19 [Google Scholar]
  92. Lee Y, Jeon K, Lee JT, Kim S, Kim VN. 2002. MicroRNA maturation: stepwise processing and subcellular localization. EMBO J 21:4663–70 [Google Scholar]
  93. Lee YS, Dutta A. 2007. The tumor suppressor microRNA let-7 represses the HMGA2 oncogene. Genes Dev 21:1025–30 [Google Scholar]
  94. Lee YS, Shibata Y, Malhotra A, Dutta A. 2009. A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev 23:2639–49 [Google Scholar]
  95. Lewis BP, Burge CB, Bartel DP. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15–20 [Google Scholar]
  96. Li J, Yang J, Zhou P, Le Y, Zhou C. et al. 2015. Circular RNAs in cancer: novel insights into origins, properties, functions and implications. Am. J. Cancer Res. 5:472–80 [Google Scholar]
  97. Li Y, Choi PS, Casey SC, Dill DL, Felsher DW. 2014. MYC through miR-17–92 suppresses specific target genes to maintain survival, autonomous proliferation, and a neoplastic state. Cancer Cell 26:262–72 [Google Scholar]
  98. Li Z, Rana TM. 2014. Therapeutic targeting of microRNAs: current status and future challenges. Nat. Rev. Drug Discov. 13:622–38 [Google Scholar]
  99. Liao DJ, Du Q-Q, Yu BW, Grignon D, Sarkar FH. 2003. Novel perspective: focusing on the X chromosome in reproductive cancers. Cancer Invest 21:641–58 [Google Scholar]
  100. Lin S, Gregory RI. 2015. MicroRNA biogenesis pathways in cancer. Nat. Rev. Cancer 15:321–33 [Google Scholar]
  101. Liz J, Portela A, Soler M, Gómez A, Ling H. et al. 2014. Regulation of pri-miRNA processing by a long noncoding RNA transcribed from an ultraconserved region. Mol. Cell 55:138–47 [Google Scholar]
  102. Lu Y, Thomson JM, Wong HYF, Hammond SM, Hogan BLM. 2007. Transgenic over-expression of the microRNA miR-17–92 cluster promotes proliferation and inhibits differentiation of lung epithelial progenitor cells. Dev. Biol. 310:442–53 [Google Scholar]
  103. Magistri M, Faghihi MA, St. Laurent G, Wahlestedt C. 2012. Regulation of chromatin structure by long noncoding RNAs: focus on natural antisense transcripts. Trends Genet. 28:389–96 [Google Scholar]
  104. Mannoor K, Liao J, Jiang F. 2012. Small nucleolar RNAs in cancer. Biochim. Biophys. Acta 1826:121–28 [Google Scholar]
  105. Marahrens Y, Panning B, Dausman J, Strauss W, Jaenisch R. 1997. Xist-deficient mice are defective in dosage compensation but not spermatogenesis. Genes Dev 11:156–66 [Google Scholar]
  106. Mashima R. 2015. Physiological roles of miR-155. Immunology 145:323–33 [Google Scholar]
  107. Maute RL, Schneider C, Sumazin P, Holmes A, Califano A. et al. 2013. tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma. PNAS 110:1404–9 [Google Scholar]
  108. Mavrakis KJ, Wolfe AL, Oricchio E, Palomero T, de Keersmaecker K. et al. 2010. Genome-wide RNA-mediated interference screen identifies miR-19 targets in Notch-induced T-cell acute lymphoblastic leukaemia. Nat. Cell Biol. 12:372–79 [Google Scholar]
  109. Mayr C, Hemann MT, Bartel DP. 2007. Disrupting the pairing between let-7 and Hmga2 enhances oncogenic transformation. Science 315:1576–79 [Google Scholar]
  110. McArthur K, Feng B, Wu Y, Chen S, Chakrabarti S. 2011. MicroRNA-200b regulates vascular endothelial growth factor-mediated alterations in diabetic retinopathy. Diabetes 60:1314–23 [Google Scholar]
  111. McHugh CA, Chen CK, Chow A, Surka CF, Tran C. et al. 2015. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature 521:232–36 [Google Scholar]
  112. Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J. et al. 2013. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495:333–38 [Google Scholar]
  113. Morris AR, Mukherjee N, Keene JD. 2008. Ribonomic analysis of human Pum1 reveals cis-trans conservation across species despite evolution of diverse mRNA target sets. Mol. Cell. Biol. 28:4093–103 [Google Scholar]
  114. Moyano M, Stefani G. 2015. piRNA involvement in genome stability and human cancer. J. Hematol. Oncol. 8:38 [Google Scholar]
  115. Mu P, Han Y-C, Betel D, Yao E, Squatrito M. et al. 2009. Genetic dissection of the miR-17∼92 cluster of microRNAs in Myc-induced B-cell lymphomas. Genes Dev 23:2806–11 [Google Scholar]
  116. Nakagawa S, Ip JY, Shioi G, Tripathi V, Zong X. et al. 2012. Malat1 is not an essential component of nuclear speckles in mice. RNA 18:1487–99 [Google Scholar]
  117. Nakanishi K, Weinberg DE, Bartel DP, Patel DJ. 2012. Structure of yeast Argonaute with guide RNA. Nature 486:368–74 [Google Scholar]
  118. Newman MA, Thomson JM, Hammond SM. 2008. Lin-28 interaction with the Let-7 precursor loop mediates regulated microRNA processing. RNA 14:1539–49 [Google Scholar]
  119. Ng KW, Anderson C, Marshall EA, Minatel BC, Enfield KSS. et al. 2016. Piwi-interacting RNAs in cancer: emerging functions and clinical utility. Mol. Cancer 15:5 [Google Scholar]
  120. Nora EP, Heard E. 2010. Chromatin structure and nuclear organization dynamics during X-chromosome inactivation. Cold Spring Harb. Symp. Quant. Biol. 75:333–44 [Google Scholar]
  121. O'Connell RM, Chaudhuri AA, Rao DS, Baltimore D. 2009. Inositol phosphatase SHIP1 is a primary target of miR-155. PNAS 106:7113–18 [Google Scholar]
  122. O'Connell RM, Rao DS, Chaudhuri AA, Boldin MP, Taganov KD. et al. 2008. Sustained expression of microRNA-155 in hematopoietic stem cells causes a myeloproliferative disorder. J. Exp. Med. 205:585–94 [Google Scholar]
  123. O'Connell RM, Taganov KD, Boldin MP, Cheng G, Baltimore D. 2007. MicroRNA-155 is induced during the macrophage inflammatory response. PNAS 104:1604–9 [Google Scholar]
  124. O'Donnell KA, Wentzel EA, Zeller KI, Dang CV, Mendell JT. et al. 2005. c-Myc-regulated microRNAs modulate E2F1 expression. Nature 435:839–43 [Google Scholar]
  125. Okada N, Lin C-P, Ribeiro MC, Biton A, Lai G. et al. 2014. A positive feedback between p53 and miR-34 miRNAs mediates tumor suppression. Genes Dev 28:438–50 [Google Scholar]
  126. Olive V, Bennett MJ, Walker JC, Ma C, Jiang I. et al. 2009. miR-19 is a key oncogenic component of mir-17-92. Genes Dev. 23:2839–49 [Google Scholar]
  127. Olive V, Sabio E, Bennett MJ, De Jong CS, Biton A. et al. 2013. A component of the mir-17-92 polycistronic oncomir promotes oncogene-dependent apoptosis. eLife 2:e00822 [Google Scholar]
  128. Olsen PH, Ambros V. 1999. The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev. Biol. 216:671–80 [Google Scholar]
  129. Orellana EA, Kasinski AL. 2015. MicroRNAs in cancer: a historical perspective on the path from discovery to therapy. Cancers 7:1388–1405 [Google Scholar]
  130. Ota A, Tagawa H, Karnan S, Tsuzuki S, Karpas A. et al. 2004. Identification and characterization of a novel gene, C13orf25, as a target for 13q31-q32 amplification in malignant lymphoma. Cancer Res 64:3087–95 [Google Scholar]
  131. Park SM, Gaur AB, Lengyel E, Peter ME. 2008. The miR-200 family determines the epithelial phenotype of cancer cells by targeting the E-cadherin repressors ZEB1 and ZEB2. Genes Dev 22:894–907 [Google Scholar]
  132. Pasmant E, Sabbagh A, Vidaud M, Bieche I. 2011. ANRIL, a long, noncoding RNA, is an unexpected major hotspot in GWAS. FASEB J 25:444–48 [Google Scholar]
  133. Pecot CV, Rupaimoole R, Yang D, Akbani R, Ivan C. et al. 2013. Tumour angiogenesis regulation by the miR-200 family. Nat. Commun. 4:2427 [Google Scholar]
  134. Peng JC, Shen J, Ran ZH. 2013. Transcribed ultraconserved region in human cancers. RNA Biol 10:1771–77 [Google Scholar]
  135. Pichler M, Calin GA. 2015. MicroRNAs in cancer: from developmental genes in worms to their clinical application in patients. Br. J. Cancer 113:569–73 [Google Scholar]
  136. Piskounova E, Polytarchou C, Thornton JE, LaPierre RJ, Pothoulakis C. et al. 2011. Lin28A and Lin28B inhibit let-7 microRNA biogenesis by distinct mechanisms. Cell 147:1066–79 [Google Scholar]
  137. Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP. 2010. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465:1033–38 [Google Scholar]
  138. Qiu J-J, Wang Y, Liu Y-L, Zhang Y, Ding J-X, Hua K-Q. 2016. The long non-coding RNA ANRIL promotes proliferation and cell cycle progression and inhibits apoptosis and senescence in epithelial ovarian cancer. Oncotarget 7:43256–66 [Google Scholar]
  139. Quinn JJ, Chang HY. 2016. Unique features of long non-coding RNA biogenesis and function. Nat. Rev. Genet. 17:47–62 [Google Scholar]
  140. Rack KA, Chelly J, Gibbons RJ, Rider S, Benjamin D. et al. 1994. Absence of the XIST gene from late-replicating isodicentric X chromosomes in leukaemia. Hum. Mol. Genet. 3:1053–59 [Google Scholar]
  141. Rakheja D, Chen KS, Liu Y, Shukla AA, Schmid V. et al. 2014. Somatic mutations in DROSHA and DICER1 impair microRNA biogenesis through distinct mechanisms in Wilms tumours. Nat. Commun. 2:4802 [Google Scholar]
  142. Raver-Shapira N, Marciano E, Meiri E, Spector Y, Rosenfeld N. et al. 2007. Transcriptional activation of miR-34a contributes to p53-mediated apoptosis. Mol. Cell 26:731–43 [Google Scholar]
  143. Rokavec M, Öner MG, Li H, Jackstadt R, Jiang L. et al. 2014. IL-6R/STAT3/miR-34a feedback loop promotes EMT-mediated colorectal cancer invasion and metastasis. J. Clin. Invest. 124:1853–67 [Google Scholar]
  144. Ross RJ, Weiner MM, Lin H. 2014. PIWI proteins and PIWI-interacting RNAs in the soma. Nature 505:353–59 [Google Scholar]
  145. Roybal JD, Zang Y, Ahn Y-H, Yang Y, Gibbons DL. et al. 2011. miR-200 inhibits lung adenocarcinoma cell invasion and metastasis by targeting Flt1/VEGFR1. Mol. Cancer Res. 9:25–35 [Google Scholar]
  146. Royds JA, Pilbrow AP, Ahn A, Morrin HR, Frampton C. et al. 2015. The rs11515 polymorphism is more frequent and associated with aggressive breast tumors with increased ANRIL and decreased p16INK4a expression. Front. Oncol. 5:306 [Google Scholar]
  147. Sasidharan R, Gerstein M. 2008. Genomics: Protein fossils live on as RNA. Nature 453:729–31 [Google Scholar]
  148. Schirle NT, Sheu-Gruttadauria J, MacRae IJ. 2014. Structural basis for microRNA targeting. Science 346:608–13 [Google Scholar]
  149. Schmitt AM, Chang HY. 2016. Long noncoding RNAs in cancer pathways. Cancer Cell 29:452–63 [Google Scholar]
  150. Selbach M, Schwanhäusser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N. 2008. Widespread changes in protein synthesis induced by microRNAs. Nature 455:58–63 [Google Scholar]
  151. Sharpless NE. 2005. INK4a/ARF: a multifunctional tumor suppressor locus. Mutat. Res. 576:22–38 [Google Scholar]
  152. Shi X, Nie F, Wang Z, Sun M. 2016. Pseudogene-expressed RNAs: a new frontier in cancers. Tumour Biol 37:1471–78 [Google Scholar]
  153. Spitale RC, Crisalli P, Flynn RA, Torre EA, Kool ET. et al. 2013. RNA SHAPE analysis in living cells. Nat. Chem. Biol. 9:18–20 [Google Scholar]
  154. Sun X, Liu J, Xu C, Tang S-C, Ren H. 2016. The insights of Let-7 miRNAs in oncogenesis and stem cell potency. J. Cell. Mol. Med. 20:1779–88 [Google Scholar]
  155. Tagawa H, Seto M. 2005. A microRNA cluster as a target of genomic amplification in malignant lymphoma. Leukemia 19:2013–16 [Google Scholar]
  156. Takakura S, Mitsutake N, Nakashima M, Namba H, Saenko VA. 2008. Oncogenic role of miR-17-92 cluster in anaplastic thyroid cancer cells. Cancer Sci 99:1147–54 [Google Scholar]
  157. Tam OH, Aravin AA, Stein P, Girard A, Murchison EP. et al. 2008. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 453:534–38 [Google Scholar]
  158. Tam W, Ben-Yehuda D, Hayward WS. 1997. bic, a novel gene activated by proviral insertions in avian leukosis virus-induced lymphomas, is likely to function through its noncoding RNA. Mol. Cell. Biol. 17:1490–502 [Google Scholar]
  159. Tan JY, Marques AC. 2016. miRNA-mediated crosstalk between transcripts: the missing “linc”?. BioEssays 38:295–301 [Google Scholar]
  160. Tarasov V, Jung P, Verdoodt B, Lodygin D, Epanchintsev A. et al. 2007. Differential regulation of microRNAs by p53 revealed by massively parallel sequencing: miR-34a is a p53 target that induces apoptosis and G1-arrest. Cell Cycle 6:1586–93 [Google Scholar]
  161. Thompson DM, Parker R. 2009. Stressing out over tRNA cleavage. Cell 138:215–19 [Google Scholar]
  162. Thomson JM, Newman M, Parker JS, Morin-Kensicki EM, Wright T. et al. 2006. Extensive post-transcriptional regulation of microRNAs and its implications for cancer. Genes Dev 20:2202–7 [Google Scholar]
  163. Thorenoor N, Slaby O. 2015. Small nucleolar RNAs functioning and potential roles in cancer. Tumour Biol 36:41–53 [Google Scholar]
  164. Thornton JE, Gregory RI. 2012. How does Lin28 let-7 control development and disease. Trends Cell Biol 22:474–82 [Google Scholar]
  165. Torrezan GT, Ferreira EN, Nakahata AM, Barros BDF, Castro MTM. et al. 2014. Recurrent somatic mutation in DROSHA induces microRNA profile changes in Wilms tumour. Nat. Commun. 5:4039 [Google Scholar]
  166. Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q. et al. 2010. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol. Cell. 39:925–38 [Google Scholar]
  167. Tseng Y-Y, Moriarity BS, Gong W, Akiyama R, Tiwari A. et al. 2014. PVT1 dependence in cancer with MYC copy-number increase. Nature 512:82–86 [Google Scholar]
  168. Ulitsky I, Bartel DP. 2013. lincRNAs: genomics, evolution, and mechanisms. Cell 154:26–46 [Google Scholar]
  169. Ungewiss C, Rizvi ZH, Roybal JD, Peng DH, Gold KA. et al. 2016. The microRNA-200/Zeb1 axis regulates ECM-dependent β1-integrin/FAK signaling, cancer cell invasion and metastasis through CRKL. Sci. Rep. 6:18652 [Google Scholar]
  170. Uziel T, Karginov FV, Xie S, Parker JS, Wang Y-D. et al. 2009. The miR-17∼92 cluster collaborates with the Sonic Hedgehog pathway in medulloblastoma. PNAS 106:2812–17 [Google Scholar]
  171. Ventura A, Young AG, Winslow MM, Lintault L, Meissner A. et al. 2008. Targeted deletion reveals essential and overlapping functions of the miR-17∼92 family of miRNA clusters. Cell 132:875–86 [Google Scholar]
  172. Vigorito E, Perks KL, Abreu-Goodger C, Bunting S, Xiang Z. et al. 2007. microRNA-155 regulates the generation of immunoglobulin class-switched plasma cells. Immunity 27:847–59 [Google Scholar]
  173. Viswanathan SR, Daley GQ, Gregory RI. 2008. Selective blockade of microRNA processing by Lin28. Science 320:97–100 [Google Scholar]
  174. Wang Y, He L, Du Y, Zhu P, Huang G. et al. 2015. The long noncoding RNA lncTCF7 promotes self-renewal of human liver cancer stem cells through activation of Wnt signaling. Cell Stem Cell 16:413–25 [Google Scholar]
  175. Wang Y, Sheng G, Juranek S, Tuschl T, Patel DJ. 2008. Structure of the guide-strand-containing argonaute silencing complex. Nature 456:209–13 [Google Scholar]
  176. Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S. et al. 2008. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 453:539–43 [Google Scholar]
  177. West JA, Davis CP, Sunwoo H, Simon MD, Sadreyev RI. et al. 2014. The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites. Mol. Cell 55:791–802 [Google Scholar]
  178. Wilusz JE, Freier SM, Spector DL. 2008. 3′ end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 135:919–32 [Google Scholar]
  179. Wu MK, Sabbaghian N, Xu B, Addidou-Kalucki S, Bernard C. et al. 2013. Biallelic DICER1 mutations occur in Wilms tumours. J. Pathol. 230:154–64 [Google Scholar]
  180. Xue W, Dahlman JE, Tammela T, Khan OF, Sood S. et al. 2014. Small RNA combination therapy for lung cancer. PNAS 111:E3553–61 [Google Scholar]
  181. Yang L, Lin C, Liu W, Zhang J, Ohgi KA. et al. 2011. ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs. Cell 147:773–88 [Google Scholar]
  182. Yap KL, Li S, Muñoz-Cabello AM, Raguz S, Zeng L. et al. 2010. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol. Cell 38:662–74 [Google Scholar]
  183. Yildirim E, Kirby JE, Brown DE, Mercier FE, Sadreyev RI. et al. 2013. Xist RNA is a potent suppressor of hematologic cancer in mice. Cell 152:727–42 [Google Scholar]
  184. Yoshimoto R, Mayeda A, Yoshida M, Nakagawa S. 2016. MALAT1 long non-coding RNA in cancer. Biochim. Biophys. Acta 1859:192–99 [Google Scholar]
  185. Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J. et al. 2008. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451:202–6 [Google Scholar]
  186. Zhang B, Arun G, Mao YS, Lazar Z, Hung G. et al. 2012. The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Rep. 2:111–23 [Google Scholar]
  187. Zhang Y, Roccaro AM, Rombaoa C, Flores L, Obad S. et al. 2012. LNA-mediated anti-miR-155 silencing in low-grade B-cell lymphomas. Blood 120:1678–86 [Google Scholar]
  188. Zhao Z-J, Shen J. 2016. Circular RNA participates in the carcinogenesis and the malignant behavior of cancer. RNA Biol. In press [Google Scholar]
  189. Zhou H, Huang X, Cui H, Luo X, Tang Y. et al. 2010. miR-155 and its star-form partner miR-155* cooperatively regulate type I interferon production by human plasmacytoid dendritic cells. Blood 116:5885–94 [Google Scholar]
  190. Zhu H, Han C, Wu T. 2015. MiR-17-92 cluster promotes hepatocarcinogenesis. Carcinogenesis 36:1213–22 [Google Scholar]
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